compare_genes_in_cell_state

Compares gene expression levels in a given cell state with its parent, sibling, and child states, and interprets the resulting patterns.

compare_genes_in_cell_state(
  cell_state,
  state_graph,
  estimate_matrix,
  stderr_matrix,
  n,
  state_term = "cell_group",
  log_fc_thresh = 1,
  abs_expr_thresh = 0.001,
  sig_thresh = 0.05,
  cores = 1,
  expected_effect_mode_interval = c(-10, 10),
  cv_threshold = NULL
)

Arguments

• cell_state
  character
  The cell state to be analyzed.

• state_graph
  igraph
  The state graph.

• estimate_matrix
  matrix
  Per-cell-state coefficient estimates (genes x cell states).

• stderr_matrix
  matrix
  Standard errors for estimate_matrix, same shape.

• n
  numeric
  Number of pseudobulk samples the models were fit on.

• state_term
  character
  Column identifying cell states. Default is "cell_group".

• log_fc_thresh
  numeric
  Log fold change threshold. Default is 1.

• abs_expr_thresh
  numeric
  Absolute expression threshold. Default is 1e-3.

• sig_thresh
  numeric
  Significance threshold. Default is 0.05.

• cores
  numeric
  Number of cores for parallel processing. Default is 1.

• expected_effect_mode_interval
  numeric vector
  Expected effect mode interval. Default is c(-10, 10).

• cv_threshold
  numeric
  Coefficient of variation threshold. Default is NULL.

Value

A tibble containing gene expression comparisons and interpretations.

Details

Identifies the parent, sibling, and child states of cell_state in state_graph, computes gene expression levels and significance for all of them, and compares the target state against each neighbor to classify each gene's expression pattern.

Examples

condensate_genes <- compare_genes_in_cell_state(
  cell_state = "pectoral fin condensate",
  state_graph = pf_cell_state_graph@graph,
  estimate_matrix = pb_coeffs$coefficients,
  stderr_matrix = pb_coeffs$stdev.unscaled,
  n = ncol(pb_cds)
)